Contacts of the strand formed by residues 15 - 21 (chain B) in PDB entry 3VZC


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with CYS 15 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  PRO*     5.1     1.8    -      -       -      -
     11B  LEU*     4.4    16.4    -      -       -      -
     12B  PRO*     3.0    24.5    -      -       +      +
     14B  PRO*     1.3    73.7    -      -       -      +
     16B  ARG*     1.3    63.5    +      -       -      +
     17B  VAL*     4.5     5.8    -      -       -      -
     46B  GLU      3.3     3.1    +      -       -      +
     47B  ILE*     3.7    22.0    -      -       -      -
     48B  SER*     3.0    26.7    +      -       -      +
     73B  ASP*     3.3    22.9    -      -       +      +
    145B  ARG*     3.6    18.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  GLU*     2.7    38.8    +      -       -      -
    244A  PRO*     5.9     0.2    -      -       -      +
     15B  CYS*     1.3    77.6    -      -       -      +
     17B  VAL*     1.3    64.2    +      -       -      +
     48B  SER*     3.3    22.8    +      -       -      +
     49B  PHE*     5.7     0.2    -      -       -      -
     50B  THR*     6.4     0.2    -      -       +      -
     71B  ARG*     2.9    29.6    -      -       -      +
     72B  TRP*     4.2    13.5    -      -       +      -
     73B  ASP*     2.8    49.5    +      -       -      +
     56C  ARG*     5.2     6.3    -      -       -      +
     62C  GLU*     3.8    21.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  LEU*     5.1     0.4    -      -       +      -
     15B  CYS*     4.5     8.5    -      -       -      -
     16B  ARG*     1.3    81.1    -      -       -      +
     18B  LEU*     1.3    57.3    +      -       -      +
     19B  VAL*     3.6    15.0    -      -       +      -
     42B  LEU*     5.4     1.8    -      -       +      -
     47B  ILE*     3.9    22.0    -      -       +      -
     48B  SER      3.0     9.8    +      -       -      +
     49B  PHE*     3.1    12.3    -      -       +      -
     50B  THR      3.0    24.6    +      -       -      -
     72B  TRP*     3.6     7.2    -      -       -      -
     74B  ALA*     3.4    27.8    -      -       +      +
     76B  VAL*     3.2    31.4    -      -       +      -
    142B  LEU*     4.8     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  VAL*     1.3    71.7    -      -       -      +
     19B  VAL*     1.3    56.3    +      -       -      +
     20B  LEU*     3.7    23.2    +      -       +      +
     50B  THR*     3.6    19.3    -      -       -      +
     52B  MET*     3.7    32.1    -      -       +      -
     64B  VAL*     6.0     2.5    -      -       +      -
     67B  GLU*     4.1    18.4    -      -       +      +
     72B  TRP*     3.5    43.7    -      -       +      +
     74B  ALA      3.1     6.7    +      -       -      -
     75B  LEU*     3.4    23.4    -      -       +      +
     76B  VAL      2.7    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  VAL*     3.6    24.7    -      -       +      -
     18B  LEU*     1.3    70.5    -      -       -      +
     20B  LEU*     1.3    67.0    +      -       -      +
     21B  LEU*     3.6     6.3    +      -       +      -
     34B  PHE*     4.0    20.4    -      -       +      -
     42B  LEU*     5.1     2.7    -      -       +      -
     49B  PHE*     4.0    16.6    -      -       +      -
     50B  THR      2.9    10.3    +      -       -      +
     51B  LEU*     3.4    27.4    -      -       +      +
     52B  MET      2.9    27.2    +      -       -      +
     76B  VAL*     3.3    26.0    -      -       +      +
     78B  MET*     4.6     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  LEU*     3.7    33.2    +      -       +      +
     19B  VAL*     1.3    71.1    -      -       -      +
     21B  LEU*     1.3    59.6    +      -       -      +
     52B  MET*     3.5    27.4    -      -       +      +
     54B  THR*     4.4     5.4    -      -       +      -
     60B  ALA*     4.2    15.7    -      -       +      +
     63B  LEU*     5.5     4.9    -      -       +      -
     64B  VAL*     3.9    17.9    -      -       +      -
     75B  LEU*     5.6     5.2    -      -       +      -
     76B  VAL      2.9    13.9    +      -       -      +
     77B  VAL*     3.5     3.2    -      -       +      -
     78B  MET*     2.9    25.6    +      -       -      +
     83B  LEU*     3.6    14.7    -      -       +      +
     87B  VAL*     3.5    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     3.6     7.8    +      -       +      +
     20B  LEU*     1.3    75.2    -      -       -      +
     22B  ASN*     1.3    75.5    +      -       -      +
     23B  PRO*     3.3    17.5    -      -       +      +
     30B  ALA*     3.8    10.5    -      -       +      +
     31B  LEU*     3.8    23.3    -      -       +      +
     34B  PHE*     3.7    30.5    -      -       +      -
     51B  LEU*     4.0    17.7    -      -       +      -
     52B  MET      3.2     7.5    +      -       -      +
     53B  LEU*     3.4    15.0    -      -       +      -
     54B  THR*     2.9    25.2    +      -       -      +
     78B  MET*     3.5    25.6    -      -       +      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il